Wednesday, December 17, 2014

Back to Richard Zander's Framework: about a book review

Richard Zander, the author of the Framework for Post-Phylogenetic Systematics (which I reviewed for a society newsletter, see also my blog posts here, here, here, here and here) is outraged by what he calls a “particularly nasty” review of his book by Andrew Brower in the journal Cladistics. Of course his book was never going to be received well by this bastion of the school of systematics he is most aggressively opposed to, but he complains that the review “lacks understanding and collegial dignity”.

He submitted a supposedly “light-hearted” response to Cladistics but was turned down; and although they may exist somewhere I cannot remember ever having seen a rebuttal to any book review in any journal before, so that does not surprise me. His reply can therefore be found in Phytoneuron, a journal that I had never heard of before. It seems to be an online-only, one man operation, whose review process is described as follows (accessed 17 December 2014):
Submissions will be promptly reviewed for content and style by the editor, based on his own knowledge and expertise. If deemed appropriate or necessary by the editor, or if requested by the author, review by other botanical peers will be sought.
Zander's reply consists mostly of a complaint about Brower's “disparagements” and two arguments by analogy; the latter I found so bizarre that I felt motivated to write this post. First, however, the tone.

Monday, December 15, 2014

Trying to use SNAPP

I really should rewrite my post on species tree methods one of these days. But at the moment I do not have the energy, and so I will simply write a few words on my experience with SNAPP.

Anybody who happens upon my species tree methods post will see that despite being more of a parsimony guy myself I have a lot of praise for BEAST. It is fast (for a Bayesian method) and very user-friendly. "Normal" BEAST is for standard gene tree phylogenetics, *BEAST or starBEAST is the add-on for species tree analyses based on multiple independent genes, and the still fairly novel SNAPP is the add-on for species tree analyses based on Single Nucleotide Polymorphism (SNP) data.

With genomic sequencing, SNPs are only going to become more important for the study of closely related organisms. If you have species that are very recently derived, any individual gene sequence is probably going to be extremely similar between them. This means that the approach of inferring species trees from the reconciliation of multiple gene trees is unlikely to work: instead of gene trees you are likely to get gene "combs", simply unresolved relationships.

There will still be thousands of little individual mutations differentiating your study specimens, but they will be distributed all across their genomes. This is why they are called SNPs: Single Nucleotide Polymorphisms each surrounded by conserved sequence regions.

The idea of SNAPP is now to use the SNPs from multiple samples per species directly to infer the species phylogeny, without any intermediate steps like alignments or gene trees. For this, it uses the coalescent model and the usual Bayesian Marcov Chain Monte Carlo approach. This sounds very attractive, especially after the good experiences with BEAST, and also very rigorous.

Unfortunately, so far my attempts at using SNAPP have been rather frustrating. There are three main issues:
  • SNAPP appears to be rather capricious as to whether it will run at all or whether it will fall over. The only machine on which I can get it to run consistently is our family computer, a Linux machine. On the Windows machine at work it is also very consistent in that it always error messages and crashes.
  • BEAST in general is known to have a problem with missing data although it can at least be tricked into accepting an allele missing for a species. Still, the same problem applies to SNAPP; a colleague had to throw out most of the data and samples he had to get missing data below ca. 5% before he could do an analysis. In my dataset that is just not possible, I'd be left with too few SNPs.
  • Finally, SNAPP is really. Really. Really. Slow. A hundred SNPs, no problem, I can run a decent analysis over a day. Five hundred SNPs? Forget it. Our high performance computing cluster at work did 1,000 generations over a few hours, and I need it to do at least ten million generations; do the math. At home I just tried a dataset reduced to 200 SNPs, and it seems as if it will finish in three months. All that sounds like First World Problems, but the thing is, the whole point of genome-wide SNPs is that you have thousands of them. A SNAPP analysis of my whole dataset is just not going to happen, even if I did not have the missing data issue on top of it.
I will see what I can do, but at the moment this new piece of software seems to be a realistic option only for rather small datasets, on the lines of the Amplified Fragment Length Polymorphisms I generated for my Ph.D. more than a decade ago...

'Evolutionary' classifications still do not have any information content (that special issue on paraphyly)

(The following is the fourth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Next we come to the contribution written by Elvira Hörandl (2014). I could say that the paper is a strange thing, but then again most of them are seeing as how they generally do not fall into the usual categories of publications in my area, either original research or review articles. In the present case, the paper could perhaps most accurately be described as a review article, but one looking back not, as usual, across a rich and productive field that the author now attempts to summarise, but looking back instead onto a single previous publication: a classification of the buttercup genus Ranunculus also published by herself (Hörandl & Emadzade, 2012).

This means that except for lacking the methods section and extensive supplementary material this paper has pretty much the same content as that earlier publication: it describes the exact same classification and extols it as superior to one that would accept only monophyletic taxa. It contains much rapid-fire criticism of phylogenetic systematics but mostly revolves around two central claims, and it is those two which I will focus on in this post.

Thursday, December 11, 2014

Botany Picture #187: Nertera granadensis


Nertera granadensis (Rubiaceae), Argentina, 2009. This little creeping plant is apparently a popular ornamental as a ground-cover. This picture, however, was taken in the wild near Bariloche.

Tuesday, December 9, 2014

Intelligence is not actually magic

Reading once more a discussion of the singularitarian movement Less Wrong, it occurs to me that the principal mistake of singularitarians is not actually their belief in accelerating and unbounded progress. Yes, they are wrong about that too, but the core mistake is this:

They believe that intelligence is a kind of magic pixie dust that enables the being exhibiting that intelligence to achieve, well, pretty much everything it can imagine.

That is really at the core of their fear of hostile artificial super-intelligence, and of their hope for the fruits of building a friendly artificial super-intelligence. They believe that if somebody builds a sufficiently clever supercomputer then this supercomputer can achieve anything. Immortality. Space flight. Free energy. Exterminating all of humanity. Feeding all of humanity. And a pony.

A simple thought experiment should set this straight. Imagine a small island in the middle of the ocean. It is just a bare rock, without any plants, animals, iron ore, coal or whatever resources beyond rock. Now plop down on this island the superest super-intelligence you can just about imagine, and imagine that it wants to leave the island.

Will it succeed? Well no. How could it? There are no resources whatsoever, and rocks don't swim.

The same principle applies if we swap the island for our planet. It is well possible that no matter how super-intelligent a friendly intelligence is, there will still not be enough resources on this planet to work out a way to provide eight billion humans with a lifestyle that is both comfortable and sustainable.

It is well possible that it is quite simply physically impossible for a fragile biological organism to fly to a distant star and survive the journey, full stop, and that even a super-intelligence could only concede that fact.

It is well possible that immortality, even as "brain-uploading", is an unachievable dream, and that even a super-intelligence could only concede that fact.

It is well possible that fusion power cannot be produced economically outside of a star, and that even a super-intelligence could only concede that fact.

And it is actually pretty likely that an evil artificial super-intelligence could be stopped in its tracks by taking an axe to its power supply, just like the most intelligent human could be knocked out or shot by one of the stupidest.

Because intelligence is not magic pixie dust. It is perhaps best defined as the capability to solve problems efficiently, but it cannot solve unsolvable problems, and it does not somehow make the laws of physics go away.

Monday, December 8, 2014

The word paraphyletic still doesn't apply to groups of sexually reproducing individuals (that special issue on paraphyly)

(The following is the third part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Although I have yet to read through all of them, I can already say that the first proper paper in the special issue, Lockhart et al.'s “We are still learning about thenature of species and their evolutionary relationships”, seems a bit out of place. This is because in contrast to several of the other contributions it is not a personally offended, unstructured, rambling Gish Gallop that attempts to fling anything and everything at that upstart cladism in the hope that something will stick, but instead focuses mostly on one idea: there might be ongoing gene flow between the entities we currently recognise as species, and therefore the currently used coalescent species tree methods might be inappropriate to reconstruct phylogenies in those situations.

If that were it, one could happily agree, all cladists could happily agree, and we could call it a day. However, this paper was submitted as a contribution to Stuessy & Hörandl's campaign for the recognition of paraphyletic supraspecific taxa, and so the clear implication is that the observation of occasional introgression between closely related species somehow means we should not classify organisms by their relatedness. The other authors of the special issue will surely cite this paper as supportive of that position over the next few years, and Lockhart et al. must be aware of that.

Saturday, December 6, 2014

Sectarianism


On a little field trip yesterday I saw what must have been the saddest cemetery I ever visited. A straight path across a weedy lawn, and at intervals there were sign posts pointing off to the sides: Catholic; Anglican; Methodist; Jewish; Independent.

Are different sects so icky that the religious have to keep them apart even in death? I am an atheist, but I would not have any problem with being buried between a fundamentalist Muslim and a Scientologist. Who cares? We are all humans.

And that poor Methodist grave. There was but a single one in that area, all alone by itself.